Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-23 14:05:57 -0400 (Sat, 23 Oct 2021).

CHECK results for dce on nebbiolo2

To the developers/maintainers of the dce package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/dce.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 454/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dce 1.1.0  (landing page)
Kim Philipp Jablonski
Snapshot Date: 2021-10-22 14:50:11 -0400 (Fri, 22 Oct 2021)
git_url: https://git.bioconductor.org/packages/dce
git_branch: master
git_last_commit: 56b47a6
git_last_commit_date: 2021-05-19 13:00:18 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: dce
Version: 1.1.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:dce.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings dce_1.1.0.tar.gz
StartedAt: 2021-10-22 19:43:59 -0400 (Fri, 22 Oct 2021)
EndedAt: 2021-10-22 19:48:38 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 279.1 seconds
RetCode: 0
Status:   OK  
CheckDir: dce.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:dce.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings dce_1.1.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/dce.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dce/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dce’ version ‘1.1.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘dce’ 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 ... NOTE
as.data.frame.dce: no visible binding for global variable ‘.’
graph2df: no visible binding for global variable ‘.’
plot_network: no visible global function definition for ‘%T>%’
plot_network: no visible binding for global variable ‘.’
Undefined global functions or variables:
  %T>% .
* 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 ... NOTE
  Note: found 6 marked UTF-8 strings
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/dce.Rcheck/00check.log’
for details.



Installation output

dce.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL dce
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘dce’ ...
** 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 (dce)

Tests output

dce.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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(dce)

> library(igraph)

Attaching package: 'igraph'

The following object is masked from 'package:testthat':

    compare

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

> library(tidyverse)
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
✔ ggplot2 3.3.5     ✔ purrr   0.3.4
✔ tibble  3.1.5     ✔ dplyr   1.0.7
✔ tidyr   1.1.4     ✔ stringr 1.4.0
✔ readr   2.0.2     ✔ forcats 0.5.1
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::as_data_frame() masks tibble::as_data_frame(), igraph::as_data_frame()
✖ purrr::compose()       masks igraph::compose()
✖ tidyr::crossing()      masks igraph::crossing()
✖ readr::edition_get()   masks testthat::edition_get()
✖ dplyr::filter()        masks stats::filter()
✖ dplyr::groups()        masks igraph::groups()
✖ purrr::is_null()       masks testthat::is_null()
✖ dplyr::lag()           masks stats::lag()
✖ readr::local_edition() masks testthat::local_edition()
✖ dplyr::matches()       masks tidyr::matches(), testthat::matches()
✖ purrr::simplify()      masks igraph::simplify()
> 
> 
> test_check("dce")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (5)

[ FAIL 0 | WARN 201 | SKIP 5 | PASS 40028 ]
> 
> proc.time()
   user  system elapsed 
 67.877   2.286  70.157 

Example timings

dce.Rcheck/dce-Ex.timings

nameusersystemelapsed
as.data.frame.dce2.0550.0762.131
as_adjmat0.0400.0080.048
create_random_DAG0.0960.0440.140
dce-methods1.1190.2081.328
dce_nb2.9980.4483.446
estimate_latent_count0.9150.0320.946
g2dag0.1940.0040.199
get_pathway_info0.3340.0040.338
get_pathways4.3230.0644.386
get_prediction_counts0.0010.0000.002
graph2df0.0310.0000.032
graph_union0.0630.0000.063
pcor0.0030.0000.002
permutation_test0.0230.0000.023
plot.dce0.6460.0080.655
plot_network0.1870.0000.186
propagate_gene_edges0.1130.0000.113
resample_edge_weights0.0040.0000.004
simulate_data-methods0.0240.0000.024
topologically_ordering000
trueEffects0.0040.0000.004