Sara Ballouz
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/EGAD |
| Branch: RELEASE_3_7 |
| Last Commit: 1b82d8e |
| Last Changed Date: 2018-07-24 11:18:57 -0400 (Tue, 24 Jul 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:28:59 -0400 (Wed, 17 Oct 2018).
| Package 436/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| EGAD 1.8.0 Sara Ballouz
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: EGAD |
| Version: 1.8.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:EGAD.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings EGAD_1.8.0.tar.gz |
| StartedAt: 2018-10-16 00:05:14 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 00:08:23 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 188.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: EGAD.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:EGAD.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings EGAD_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/EGAD.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EGAD/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EGAD’ version ‘1.8.0’
* 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 ‘EGAD’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 41.4Mb
sub-directories of 1Mb or more:
data 41.2Mb
* 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 ... NOTE
Namespace in Imports field not imported from: ‘affy’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
assortativity: no visible global function definition for ‘cor’
build_coexp_network: no visible global function definition for ‘cor’
conv_smoother: no visible global function definition for ‘convolve’
conv_smoother: no visible global function definition for ‘plot’
conv_smoother: no visible global function definition for ‘polygon’
conv_smoother: no visible global function definition for ‘points’
conv_smoother: no visible global function definition for ‘lines’
get_biogrid: no visible global function definition for ‘download.file’
get_biogrid: no visible global function definition for ‘unzip’
get_biogrid: no visible global function definition for ‘read.table’
get_expression_data_gemma: no visible global function definition for
‘read.table’
get_expression_matrix_from_GEO: no visible global function definition
for ‘median’
get_expression_matrix_from_GEO: no visible global function definition
for ‘aggregate’
get_expression_matrix_from_GEO: no visible binding for global variable
‘median’
get_phenocarta: no visible global function definition for ‘read.table’
make_transparent: no visible global function definition for ‘col2rgb’
make_transparent : <anonymous>: no visible global function definition
for ‘rgb’
plot_densities: no visible global function definition for ‘plot’
plot_densities : <anonymous>: no visible global function definition for
‘polygon’
plot_densities : <anonymous>: no visible global function definition for
‘lines’
plot_density_compare: no visible global function definition for
‘density’
plot_density_compare: no visible global function definition for ‘plot’
plot_density_compare: no visible global function definition for
‘polygon’
plot_density_compare: no visible global function definition for ‘lines’
plot_distribution: no visible global function definition for ‘hist’
plot_distribution: no visible global function definition for ‘boxplot’
plot_distribution: no visible global function definition for ‘plot’
plot_distribution: no visible global function definition for ‘polygon’
plot_distribution: no visible global function definition for ‘lines’
plot_distribution: no visible global function definition for ‘abline’
plot_prc: no visible global function definition for ‘plot’
plot_prc: no visible global function definition for ‘abline’
plot_roc: no visible global function definition for ‘plot’
plot_roc_overlay: no visible global function definition for ‘axis’
plot_roc_overlay: no visible global function definition for ‘lines’
plot_value_compare: no visible global function definition for ‘plot’
plot_value_compare: no visible global function definition for ‘abline’
Undefined global functions or variables:
abline aggregate axis boxplot col2rgb convolve cor density
download.file hist lines median plot points polygon read.table rgb
unzip
Consider adding
importFrom("grDevices", "col2rgb", "rgb")
importFrom("graphics", "abline", "axis", "boxplot", "hist", "lines",
"plot", "points", "polygon")
importFrom("stats", "aggregate", "convolve", "cor", "density",
"median")
importFrom("utils", "download.file", "read.table", "unzip")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'conv_smoother':
conv_smoother
Code: function(X, Y, window, raw = FALSE, output = FALSE, ...)
Docs: function(X, Y, window, xlab = "", ylab = "", raw = FALSE)
Argument names in code not in docs:
output ...
Argument names in docs not in code:
xlab ylab
Mismatches in argument names:
Position: 4 Code: raw Docs: xlab
Position: 5 Code: output Docs: ylab
Position: 6 Code: ... Docs: raw
* 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 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: 1 WARNING, 3 NOTEs
See
‘/home/biocbuild/bbs-3.7-bioc/meat/EGAD.Rcheck/00check.log’
for details.
EGAD.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL EGAD ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘EGAD’ ... ** 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 * DONE (EGAD)
EGAD.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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(EGAD)
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
>
> test_check("EGAD")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 9 SKIPPED: 2 FAILED: 0
>
> proc.time()
user system elapsed
6.500 0.208 7.375
EGAD.Rcheck/EGAD-Ex.timings
| name | user | system | elapsed | |
| assortativity | 0.000 | 0.000 | 0.002 | |
| auc_multifunc | 0.000 | 0.000 | 0.002 | |
| auprc | 0.004 | 0.000 | 0.004 | |
| auroc_analytic | 0 | 0 | 0 | |
| build_binary_network | 0.004 | 0.000 | 0.002 | |
| build_coexp_expressionSet | 0.004 | 0.000 | 0.004 | |
| build_coexp_network | 0.004 | 0.000 | 0.005 | |
| build_semantic_similarity_network | 0.004 | 0.000 | 0.001 | |
| build_weighted_network | 0.000 | 0.000 | 0.001 | |
| calculate_multifunc | 0.004 | 0.000 | 0.003 | |
| conv_smoother | 0.012 | 0.000 | 0.010 | |
| extend_network | 0.004 | 0.000 | 0.003 | |
| filter_network | 0.000 | 0.000 | 0.001 | |
| filter_network_cols | 0.000 | 0.000 | 0.002 | |
| filter_network_rows | 0.004 | 0.000 | 0.002 | |
| filter_orthologs | 0.004 | 0.000 | 0.002 | |
| fmeasure | 0.000 | 0.000 | 0.001 | |
| get_auc | 0.004 | 0.000 | 0.002 | |
| get_counts | 0.004 | 0.000 | 0.002 | |
| get_density | 0.000 | 0.000 | 0.001 | |
| get_prc | 0.000 | 0.000 | 0.001 | |
| get_roc | 0.000 | 0.000 | 0.001 | |
| make_annotations | 0.000 | 0.004 | 0.001 | |
| make_gene_network | 0.512 | 0.000 | 0.512 | |
| make_genelist | 0.004 | 0.000 | 0.001 | |
| neighbor_voting | 0.024 | 0.000 | 0.024 | |
| node_degree | 0.000 | 0.000 | 0.001 | |
| plot_densities | 0.020 | 0.000 | 0.018 | |
| plot_density_compare | 0.008 | 0.000 | 0.007 | |
| plot_distribution | 0.004 | 0.000 | 0.005 | |
| plot_network_heatmap | 0.032 | 0.000 | 0.031 | |
| plot_prc | 0.012 | 0.000 | 0.012 | |
| plot_roc | 0.000 | 0.000 | 0.002 | |
| plot_roc_overlay | 0.060 | 0.000 | 0.058 | |
| predictions | 0.008 | 0.000 | 0.007 | |
| repmat | 0.000 | 0.000 | 0.001 | |
| run_GBA | 0.012 | 0.000 | 0.013 | |