Sara Ballouz
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/EGAD |
| git_branch: RELEASE_3_13 |
| git_last_commit: 948910f |
| git_last_commit_date: 2021-05-19 12:20:29 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:03 -0400 (Fri, 15 Oct 2021).
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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 559/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| EGAD 1.20.0 (landing page) Sara Ballouz
| 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: EGAD |
| Version: 1.20.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EGAD.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings EGAD_1.20.0.tar.gz |
| StartedAt: 2021-10-14 22:40:21 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 22:42:34 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 132.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: EGAD.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EGAD.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings EGAD_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/EGAD.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.20.0'
* 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 39.5Mb
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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/EGAD.Rcheck/00check.log'
for details.
EGAD.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/EGAD_1.20.0.tar.gz && rm -rf EGAD.buildbin-libdir && mkdir EGAD.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=EGAD.buildbin-libdir EGAD_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL EGAD_1.20.0.zip && rm EGAD_1.20.0.tar.gz EGAD_1.20.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
8 14.5M 8 1269k 0 0 668k 0 0:00:22 0:00:01 0:00:21 668k
20 14.5M 20 3011k 0 0 1031k 0 0:00:14 0:00:02 0:00:12 1031k
35 14.5M 35 5243k 0 0 1329k 0 0:00:11 0:00:03 0:00:08 1329k
48 14.5M 48 7213k 0 0 1471k 0 0:00:10 0:00:04 0:00:06 1471k
64 14.5M 64 9675k 0 0 1638k 0 0:00:09 0:00:05 0:00:04 1988k
87 14.5M 87 12.6M 0 0 1885k 0 0:00:07 0:00:06 0:00:01 2349k
100 14.5M 100 14.5M 0 0 2014k 0 0:00:07 0:00:07 --:--:-- 2655k
install for i386
* 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
install for x64
* installing *source* package 'EGAD' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'EGAD' as EGAD_1.20.0.zip
* DONE (EGAD)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'EGAD' successfully unpacked and MD5 sums checked
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EGAD.Rcheck/tests_i386/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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")
== Skipped tests ===============================================================
* empty test (2)
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 9 ]
>
> proc.time()
user system elapsed
2.39 0.14 2.54
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EGAD.Rcheck/tests_x64/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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")
== Skipped tests ===============================================================
* empty test (2)
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 9 ]
>
> proc.time()
user system elapsed
2.17 0.28 2.46
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EGAD.Rcheck/examples_i386/EGAD-Ex.timings
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EGAD.Rcheck/examples_x64/EGAD-Ex.timings
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