Sara Ballouz
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/EGAD |
| git_branch: master |
| git_last_commit: d94e355 |
| git_last_commit_date: 2021-10-26 12:27:52 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:26 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
To the developers/maintainers of the EGAD package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/EGAD.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 573/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| EGAD 1.23.0 (landing page) Sara Ballouz
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: EGAD |
| Version: 1.23.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:EGAD.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings EGAD_1.23.0.tar.gz |
| StartedAt: 2022-03-17 19:00:43 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:02:09 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 85.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: EGAD.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:EGAD.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings EGAD_1.23.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/EGAD.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'EGAD/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'EGAD' version '1.23.0'
* 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 'EGAD' can be installed ... OK
* checking installed package size ... NOTE
installed size is 39.4Mb
sub-directories of 1Mb or more:
data 38.9Mb
* checking package 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 ... 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' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
'EGAD.Rmd', 'EGAD.bib', 'figures/figure_GO_comb.png',
'figures/figure_aurocs_comparisons.png',
'figures/figure_benchmark.png', 'figures/figure_degree_corr.png',
'figures/figure_indirect.png', 'figures/figure_mf.png',
'figures/figure_mf_yeast_human.png',
'figures/figure_nd_yeast_human.png', 'figures/figure_nv.png',
'figures/figure_nv_yeast_human.png', 'figures/figure_overlay.png',
'figures/figure_pheno_comb.png',
'figures/figure_pheno_degree_corr.png',
'figures/figure_pheno_mf.png', 'figures/figure_pheno_nv.png',
'figures/figure_smoother.png', 'figures/gba_schematic_resized.png',
'figures/labels_resized.png', 'figures/mf_schematic.png',
'figures/network_resized.png', 'figures/overview_resized.png'
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
'D:/biocbuild/bbs-3.15-bioc/meat/EGAD.Rcheck/00check.log'
for details.
EGAD.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL EGAD
###
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##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'EGAD' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'EGAD'
finding HTML links ... done
GO.human html
GO.mouse html
GO.voc html
assortativity html
atrr.human html
attr.mouse html
auc_multifunc html
auprc html
auroc_analytic html
biogrid html
build_binary_network html
build_coexp_GEOID html
build_coexp_expressionSet html
build_coexp_network html
build_semantic_similarity_network html
build_weighted_network html
calculate_multifunc html
conv_smoother html
example_annotations html
example_binary_network html
example_coexpression html
example_neighbor_voting html
extend_network html
filter_network html
filter_network_cols html
filter_network_rows html
filter_orthologs html
fmeasure html
genes html
get_auc html
get_biogrid html
get_counts html
get_density html
get_expression_data_gemma html
get_expression_matrix_from_GEO html
get_phenocarta html
get_prc html
get_roc html
make_annotations html
make_gene_network html
make_genelist html
make_transparent html
neighbor_voting html
node_degree html
ortho html
pheno html
plot_densities html
plot_density_compare html
plot_distribution html
plot_network_heatmap html
plot_prc html
plot_roc html
plot_roc_overlay html
plot_value_compare html
predictions html
repmat html
run_GBA html
** 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 (EGAD)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'MultiBaC' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'ppiStats' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'VariantExperiment' is missing or broken
done
EGAD.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(EGAD)
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
>
> test_check("EGAD")
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 9 ]
== Skipped tests ===============================================================
* empty test (2)
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 9 ]
>
> proc.time()
user system elapsed
1.82 0.20 2.32
EGAD.Rcheck/EGAD-Ex.timings
| name | user | system | elapsed | |
| assortativity | 0 | 0 | 0 | |
| auc_multifunc | 0 | 0 | 0 | |
| auprc | 0.01 | 0.00 | 0.02 | |
| auroc_analytic | 0 | 0 | 0 | |
| build_binary_network | 0 | 0 | 0 | |
| build_coexp_expressionSet | 0 | 0 | 0 | |
| build_coexp_network | 0 | 0 | 0 | |
| build_semantic_similarity_network | 0.02 | 0.00 | 0.01 | |
| build_weighted_network | 0 | 0 | 0 | |
| calculate_multifunc | 0 | 0 | 0 | |
| conv_smoother | 0.01 | 0.00 | 0.02 | |
| extend_network | 0 | 0 | 0 | |
| filter_network | 0 | 0 | 0 | |
| filter_network_cols | 0 | 0 | 0 | |
| filter_network_rows | 0 | 0 | 0 | |
| filter_orthologs | 0 | 0 | 0 | |
| fmeasure | 0 | 0 | 0 | |
| get_auc | 0 | 0 | 0 | |
| get_counts | 0 | 0 | 0 | |
| get_density | 0 | 0 | 0 | |
| get_prc | 0 | 0 | 0 | |
| get_roc | 0 | 0 | 0 | |
| make_annotations | 0 | 0 | 0 | |
| make_gene_network | 0 | 0 | 0 | |
| make_genelist | 0 | 0 | 0 | |
| neighbor_voting | 0.03 | 0.00 | 0.03 | |
| node_degree | 0 | 0 | 0 | |
| plot_densities | 0.05 | 0.00 | 0.04 | |
| plot_density_compare | 0.02 | 0.00 | 0.02 | |
| plot_distribution | 0 | 0 | 0 | |
| plot_network_heatmap | 0.06 | 0.00 | 0.06 | |
| plot_prc | 0 | 0 | 0 | |
| plot_roc | 0 | 0 | 0 | |
| plot_roc_overlay | 0.09 | 0.00 | 0.09 | |
| predictions | 0.02 | 0.00 | 0.02 | |
| repmat | 0 | 0 | 0 | |
| run_GBA | 0.01 | 0.00 | 0.01 | |