Anthony Federico
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/hypeR |
| Branch: RELEASE_3_11 |
| Last Commit: 21e0dc0 |
| Last Changed Date: 2020-04-27 15:24:06 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:58:42 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE hypeR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 838/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| hypeR 1.4.0 Anthony Federico
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: hypeR |
| Version: 1.4.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:hypeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings hypeR_1.4.0.tar.gz |
| StartedAt: 2020-10-17 02:05:49 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 02:09:17 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 207.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: hypeR.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:hypeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings hypeR_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/hypeR.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hypeR/DESCRIPTION’ ... OK
* this is package ‘hypeR’ version ‘1.4.0’
* 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 ‘hypeR’ can be installed ... OK
* 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 ... NOTE
.dots_plot: no visible binding for global variable ‘pval’
.dots_plot: no visible binding for global variable ‘fdr’
.dots_plot: no visible binding for global variable ‘significance’
.dots_plot: no visible binding for global variable ‘size’
.enrichment_map: no visible binding for global variable ‘pval’
.enrichment_map: no visible binding for global variable ‘fdr’
.find_members: no visible binding for global variable ‘from’
.find_members: no visible binding for global variable ‘to’
.hiearchy_map: no visible binding for global variable ‘pval’
.hiearchy_map: no visible binding for global variable ‘fdr’
.hiearchy_map : <anonymous>: no visible binding for global variable
‘label’
.hyper_enrichment: no visible global function definition for ‘is’
.ks_enrichment: no visible global function definition for ‘is’
enrichr_available: no visible binding for global variable ‘.’
ggvenn: no visible binding for global variable ‘x’
ggvenn: no visible binding for global variable ‘y’
hyp_dots: no visible global function definition for ‘is’
hyp_emap: no visible global function definition for ‘is’
hyp_hmap: no visible global function definition for ‘is’
hyp_show: no visible global function definition for ‘is’
hyp_to_excel: no visible global function definition for ‘is’
hyp_to_excel: no visible global function definition for
‘packageVersion’
hyp_to_rmd: no visible global function definition for ‘is’
hyp_to_rmd : <anonymous>: no visible global function definition for
‘is’
hyp_to_table: no visible global function definition for ‘is’
hyp_to_table: no visible global function definition for
‘packageVersion’
hyp_to_table: no visible global function definition for ‘write.table’
hypeR: no visible global function definition for ‘is’
msigdb_available: no visible binding for global variable ‘gs_cat’
msigdb_available: no visible binding for global variable ‘gs_subcat’
msigdb_download: no visible binding for global variable ‘gs_name’
msigdb_download: no visible binding for global variable ‘gene_symbol’
msigdb_download: no visible binding for global variable ‘.’
msigdb_version: no visible global function definition for
‘packageVersion’
Undefined global functions or variables:
. fdr from gene_symbol gs_cat gs_name gs_subcat is label
packageVersion pval significance size to write.table x y
Consider adding
importFrom("methods", "is")
importFrom("utils", "packageVersion", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:
Warning: 'msigdbr::msigdbr_show_species' is deprecated.
Warning: 'msigdbr::msigdbr_show_species' is deprecated.
Warning: 'msigdbr::msigdbr_show_species' is deprecated.
Warning: 'msigdbr::msigdbr_show_species' is deprecated.
Warning: 'msigdbr::msigdbr_show_species' is deprecated.
Warning: 'msigdbr::msigdbr_show_species' is deprecated.
Warning: 'msigdbr::msigdbr_show_species' is deprecated.
Warning: 'msigdbr::msigdbr_show_species' is deprecated.
Warning: 'msigdbr::msigdbr_show_species' is deprecated.
Warning: 'msigdbr::msigdbr_show_species' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
msigdb_available 22.357 1.020 23.393
hyp_hmap 5.419 0.052 5.908
enrichr_download 0.154 0.007 13.236
* 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, 1 NOTE
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/hypeR.Rcheck/00check.log’
for details.
hypeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL hypeR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘hypeR’ ... ** using staged installation ** R ** 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 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 (hypeR)
hypeR.Rcheck/tests/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(magrittr)
Attaching package: 'magrittr'
The following objects are masked from 'package:testthat':
equals, is_less_than, not
> library(hypeR)
>
> test_check("hypeR")
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══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 409 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
76.839 2.300 81.462
hypeR.Rcheck/hypeR-Ex.timings
| name | user | system | elapsed | |
| dot-format_str | 0.000 | 0.001 | 0.001 | |
| dot-string_args | 0 | 0 | 0 | |
| enrichr_available | 0.298 | 0.020 | 0.424 | |
| enrichr_download | 0.154 | 0.007 | 13.236 | |
| enrichr_gsets | 0.167 | 0.006 | 0.733 | |
| gsets | 0.002 | 0.001 | 0.002 | |
| hyp | 0.009 | 0.001 | 0.009 | |
| hyp_dots | 4.043 | 0.229 | 4.274 | |
| hyp_emap | 1.278 | 0.087 | 1.375 | |
| hyp_hmap | 5.419 | 0.052 | 5.908 | |
| hyp_show | 1.052 | 0.050 | 1.111 | |
| hyp_to_excel | 1.726 | 0.071 | 1.805 | |
| hyp_to_table | 0.861 | 0.024 | 0.890 | |
| hypeR | 0.985 | 0.040 | 1.028 | |
| hyperdb_info | 0.000 | 0.001 | 0.001 | |
| hyperdb_rgsets | 0.063 | 0.007 | 0.124 | |
| msigdb_available | 22.357 | 1.020 | 23.393 | |
| msigdb_check_species | 0.001 | 0.000 | 0.001 | |
| msigdb_download | 0.392 | 0.039 | 0.432 | |
| msigdb_gsets | 0.391 | 0.062 | 0.452 | |
| msigdb_info | 0.002 | 0.000 | 0.002 | |
| msigdb_species | 0.009 | 0.002 | 0.011 | |
| msigdb_version | 0.001 | 0.001 | 0.002 | |
| multihyp | 0.002 | 0.001 | 0.002 | |
| pvector | 0.001 | 0.001 | 0.001 | |
| rgsets | 0.007 | 0.001 | 0.008 | |