Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-07-30 15:06:20 -0400 (Fri, 30 Jul 2021).

CHECK results for dce on machv2

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 447/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dce 1.0.0  (landing page)
Kim Philipp Jablonski
Snapshot Date: 2021-07-29 04:50:02 -0400 (Thu, 29 Jul 2021)
URL: https://git.bioconductor.org/packages/dce
Branch: RELEASE_3_13
Last Commit: a66589d
Last Changed Date: 2021-05-19 13:00:18 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: dce
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:dce.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings dce_1.0.0.tar.gz
StartedAt: 2021-07-29 17:44:58 -0400 (Thu, 29 Jul 2021)
EndedAt: 2021-07-29 17:52:05 -0400 (Thu, 29 Jul 2021)
EllapsedTime: 426.7 seconds
RetCode: 0
Status:   OK  
CheckDir: dce.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:dce.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings dce_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/dce.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.0.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
get_pathways 5.585  0.087   5.682
* 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
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/dce.Rcheck/00check.log’
for details.



Installation output

dce.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL dce
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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  3.1.3     ✔ dplyr   1.0.7
✔ tidyr   1.1.3     ✔ stringr 1.4.0
✔ readr   2.0.0     ✔ 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 (2)

[ FAIL 0 | WARN 226 | SKIP 2 | PASS 40028 ]
> 
> proc.time()
   user  system elapsed 
131.406   3.040 134.517 

Example timings

dce.Rcheck/dce-Ex.timings

nameusersystemelapsed
as.data.frame.dce1.8470.0461.896
as_adjmat0.0470.0010.048
create_random_DAG0.0790.0010.080
dce-methods1.0390.0351.074
dce_nb3.7000.2393.995
estimate_latent_count1.3720.0711.445
g2dag0.3800.0290.409
get_pathway_info0.6920.0100.704
get_pathways5.5850.0875.682
get_prediction_counts0.0030.0010.003
graph2df0.0530.0030.057
graph_union0.1340.0020.137
pcor0.0040.0010.005
permutation_test0.0330.0020.034
plot.dce0.9680.0541.023
plot_network0.3110.0020.314
propagate_gene_edges0.1970.0030.201
resample_edge_weights0.0050.0000.006
simulate_data-methods0.0410.0010.041
topologically_ordering0.0010.0000.001
trueEffects0.0060.0000.006