Gwenaëlle Lemoine
| Snapshot Date: 2025-01-10 13:40 -0500 (Fri, 10 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/GWENA |
| git_branch: devel |
| git_last_commit: 19342a3 |
| git_last_commit_date: 2024-10-29 10:48:12 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-11 11:41 -0500 (Sat, 11 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4760 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4479 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4443 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4391 |
| 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 | ||||
| Package 926/2277 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GWENA 1.17.0 (landing page) Gwenaëlle Lemoine
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the GWENA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GWENA.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: GWENA |
| Version: 1.17.0 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GWENA.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings GWENA_1.17.0.tar.gz |
| StartedAt: 2025-01-11 01:51:50 -0500 (Sat, 11 Jan 2025) |
| EndedAt: 2025-01-11 02:01:25 -0500 (Sat, 11 Jan 2025) |
| EllapsedTime: 574.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GWENA.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GWENA.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings GWENA_1.17.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/GWENA.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GWENA/DESCRIPTION' ... OK
* this is package 'GWENA' version '1.17.0'
* 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 whether package 'GWENA' can be installed ... WARNING
Found the following significant warnings:
Warning: bad markup (extra space?) at compare_conditions.Rd:91:72
Warning: bad markup (extra space?) at compare_conditions.Rd:96:77
Warning: bad markup (extra space?) at compare_conditions.Rd:98:74
Warning: bad markup (extra space?) at compare_conditions.Rd:100:69
See 'E:/biocbuild/bbs-3.21-bioc/meat/GWENA.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 ... NOTE
Problems with news in 'NEWS.md':
No news entries found.
* checking code 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 ... WARNING
prepare_Rd: bad markup (extra space?) at compare_conditions.Rd:91:72
prepare_Rd: bad markup (extra space?) at compare_conditions.Rd:96:77
prepare_Rd: bad markup (extra space?) at compare_conditions.Rd:98:74
prepare_Rd: bad markup (extra space?) at compare_conditions.Rd:100:69
* checking Rd metadata ... OK
* checking Rd cross-references ...Warning: bad markup (extra space?) at compare_conditions.Rd:91:72
Warning: bad markup (extra space?) at compare_conditions.Rd:96:77
Warning: bad markup (extra space?) at compare_conditions.Rd:98:74
Warning: bad markup (extra space?) at compare_conditions.Rd:100:69
NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
build_net.Rd: adjacency.fromSimilarity
get_fit.cor.Rd: pickSoftThreshold.fromSimilarity
get_fit.expr.Rd: pickSoftThreshold.fromSimilarity
plot_module.Rd: igraph.plotting
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
z_summary 15.14 0.10 16.89
compare_conditions 9.45 0.13 10.59
plot_enrichment 1.26 0.19 9.13
bio_enrich 0.38 0.03 10.90
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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, 2 NOTEs
See
'E:/biocbuild/bbs-3.21-bioc/meat/GWENA.Rcheck/00check.log'
for details.
GWENA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL GWENA ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'GWENA' ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help Warning: bad markup (extra space?) at compare_conditions.Rd:91:72 Warning: bad markup (extra space?) at compare_conditions.Rd:96:77 Warning: bad markup (extra space?) at compare_conditions.Rd:98:74 Warning: bad markup (extra space?) at compare_conditions.Rd:100:69 *** 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 (GWENA)
GWENA.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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(GWENA)
>
> test_check("GWENA")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 278 ]
>
> proc.time()
user system elapsed
370.06 8.12 275.42
GWENA.Rcheck/GWENA-Ex.timings
| name | user | system | elapsed | |
| associate_phenotype | 0.03 | 0.00 | 0.03 | |
| bio_enrich | 0.38 | 0.03 | 10.90 | |
| build_graph_from_sq_mat | 0.12 | 0.00 | 0.13 | |
| build_net | 3.52 | 0.01 | 3.56 | |
| compare_conditions | 9.45 | 0.13 | 10.59 | |
| detect_modules | 1.81 | 0.03 | 1.86 | |
| filter_RNA_seq | 0 | 0 | 0 | |
| filter_low_var | 0.02 | 0.00 | 0.02 | |
| get_fit.cor | 0.94 | 0.00 | 0.95 | |
| get_fit.expr | 0.81 | 0.00 | 0.81 | |
| get_hub_degree | 0.07 | 0.00 | 0.06 | |
| get_hub_genes | 0 | 0 | 0 | |
| get_hub_high_co | 0 | 0 | 0 | |
| get_hub_kleinberg | 0.18 | 0.00 | 0.19 | |
| get_sub_clusters | 1.88 | 0.03 | 1.91 | |
| is_data_expr | 0 | 0 | 0 | |
| is_gost | 0.02 | 0.00 | 2.25 | |
| is_module | 0 | 0 | 0 | |
| is_network | 0 | 0 | 0 | |
| join_gost | 0.04 | 0.00 | 1.34 | |
| plot_comparison_stats | 0.22 | 0.00 | 0.22 | |
| plot_enrichment | 1.26 | 0.19 | 9.13 | |
| plot_expression_profiles | 3.13 | 0.08 | 3.20 | |
| plot_module | 0.18 | 0.00 | 0.18 | |
| plot_modules_merge | 2.02 | 0.00 | 2.02 | |
| plot_modules_phenotype | 0.56 | 0.00 | 0.56 | |
| z_summary | 15.14 | 0.10 | 16.89 | |