Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:38 -0400 (Fri, 15 Oct 2021).
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. |
Package 447/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
dce 1.0.0 (landing page) Kim Philipp Jablonski
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: dce |
Version: 1.0.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:dce.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings dce_1.0.0.tar.gz |
StartedAt: 2021-10-14 09:29:19 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 09:33:47 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 268.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: dce.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:dce.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings dce_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-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 ‘1.0.0’ * 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 * 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-3.13-bioc/meat/dce.Rcheck/00check.log’ for details.
dce.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL dce ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-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)
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 64.876 1.575 66.447
dce.Rcheck/dce-Ex.timings
name | user | system | elapsed | |
as.data.frame.dce | 1.645 | 0.324 | 1.970 | |
as_adjmat | 0.035 | 0.000 | 0.034 | |
create_random_DAG | 0.019 | 0.000 | 0.019 | |
dce-methods | 0.302 | 0.028 | 0.330 | |
dce_nb | 2.857 | 0.064 | 2.920 | |
estimate_latent_count | 0.878 | 0.024 | 0.901 | |
g2dag | 0.189 | 0.024 | 0.213 | |
get_pathway_info | 0.464 | 0.004 | 0.469 | |
get_pathways | 4.451 | 0.044 | 4.494 | |
get_prediction_counts | 0.002 | 0.000 | 0.002 | |
graph2df | 0.034 | 0.000 | 0.034 | |
graph_union | 0.067 | 0.000 | 0.067 | |
pcor | 0.004 | 0.000 | 0.004 | |
permutation_test | 0.023 | 0.004 | 0.026 | |
plot.dce | 0.648 | 0.032 | 0.680 | |
plot_network | 0.198 | 0.000 | 0.198 | |
propagate_gene_edges | 0.117 | 0.004 | 0.121 | |
resample_edge_weights | 0.004 | 0.000 | 0.004 | |
simulate_data-methods | 0.025 | 0.000 | 0.025 | |
topologically_ordering | 0 | 0 | 0 | |
trueEffects | 0.004 | 0.000 | 0.004 | |