Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:40 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the fcoex package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/fcoex.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 623/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
fcoex 1.6.0 (landing page) Tiago Lubiana
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: fcoex |
Version: 1.6.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:fcoex.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings fcoex_1.6.0.tar.gz |
StartedAt: 2021-10-14 09:49:34 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 09:53:57 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 263.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: fcoex.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:fcoex.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings fcoex_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/fcoex.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 ‘fcoex/DESCRIPTION’ ... OK * this is package ‘fcoex’ version ‘1.6.0’ * 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 ‘fcoex’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘Matrix::head’ by ‘utils::head’ when loading ‘fcoex’ See ‘/home/biocbuild/bbs-3.13-bioc/meat/fcoex.Rcheck/00install.out’ for details. * 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 ... WARNING Documented arguments not in \usage in documentation object '.plot_one_interaction': ‘...’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed find_cbf_modules 17.663 0.972 18.636 get_nets 15.833 0.100 15.934 * 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 WARNINGs See ‘/home/biocbuild/bbs-3.13-bioc/meat/fcoex.Rcheck/00check.log’ for details.
fcoex.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL fcoex ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘fcoex’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB Warning: replacing previous import ‘Matrix::head’ by ‘utils::head’ when loading ‘fcoex’ in method for ‘mod_ora’ with signature ‘"fcoex"’: no definition for class “fcoex” ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘Matrix::head’ by ‘utils::head’ when loading ‘fcoex’ in method for ‘mod_ora’ with signature ‘"fcoex"’: no definition for class “fcoex” ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘Matrix::head’ by ‘utils::head’ when loading ‘fcoex’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘Matrix::head’ by ‘utils::head’ when loading ‘fcoex’ ** testing if installed package keeps a record of temporary installation path * DONE (fcoex)
fcoex.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(fcoex) Warning message: replacing previous import 'Matrix::head' by 'utils::head' when loading 'fcoex' > > test_check("fcoex") [1] 0.1 [1] "Number of features features = 40" [1] "Number of prospective features = 14" Round 1 [1] "first_prime round ( |s_prime| = 14 )" 0.1867632 0.1586357 Removed feature 13 0.1256985 0.1198729 Removed feature 38 0.1168656 0.1068907 Removed feature 18 0.2045022 0.09770198 Removed feature 34 0.1736622 0.08930267 Removed feature 32 Round 2 [1] "first_prime round ( |s_prime| = 9 )" 0.2161864 0.1610819 Removed feature 39 Round 3 [1] "first_prime round ( |s_prime| = 8 )" 0.128325 0.1124689 Removed feature 30 Round 4 [1] "first_prime round ( |s_prime| = 7 )" Round 5 [1] "first_prime round ( |s_prime| = 7 )" Round 6 [1] "first_prime round ( |s_prime| = 7 )" Round 7 [1] "first_prime round ( |s_prime| = 7 )" [1] "Number of final features = 7" [1] "Gene-1" [1] "Gene-40" [1] "Gene-28" [1] "Gene-39" [1] "Gene-13" [1] "Gene-26" [1] "Gene-12" [1] "Gene-25" [1] "Gene-38" [1] "Gene-35" [1] "Gene-30" [1] "Gene-18" [1] "Gene-34" [1] "Gene-32" [1] "Gene-1" [1] "Gene-40" [1] "Gene-28" [1] "Gene-26" [1] "Gene-12" [1] "Gene-25" [1] "Gene-35" [ FAIL 0 | WARN 14 | SKIP 0 | PASS 4 ] > > proc.time() user system elapsed 9.431 0.418 9.837
fcoex.Rcheck/fcoex-Ex.timings
name | user | system | elapsed | |
discretize | 3.139 | 0.088 | 3.227 | |
fc | 0.213 | 0.040 | 0.253 | |
find_cbf_modules | 17.663 | 0.972 | 18.636 | |
get_nets | 15.833 | 0.100 | 15.934 | |
idents | 0.222 | 0.012 | 0.234 | |
mini_pbmc3k | 0.484 | 0.016 | 0.501 | |
mod_colors | 0.223 | 0.012 | 0.235 | |
mod_gene_num | 0.238 | 0.011 | 0.251 | |
mod_names | 0.219 | 0.031 | 0.252 | |
mod_ora | 2.111 | 0.043 | 2.155 | |
module_genes | 0.885 | 0.012 | 0.897 | |
new_fcoex | 0.219 | 0.023 | 0.243 | |
nmodules | 0.223 | 0.000 | 0.223 | |
ora_data | 0.206 | 0.035 | 0.242 | |
plot_ora | 1.988 | 0.060 | 2.048 | |
recluster | 0.437 | 0.016 | 0.453 | |
save_plots | 0.001 | 0.000 | 0.001 | |
show-fcoex-method | 0.236 | 0.011 | 0.248 | |
show_net | 0.001 | 0.000 | 0.000 | |
show_ora | 0.249 | 0.013 | 0.261 | |