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CHECK report for hypeR on malbec2

This page was generated on 2019-10-16 12:17:32 -0400 (Wed, 16 Oct 2019).

Package 777/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hypeR 1.0.0
Anthony Federico
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/hypeR
Branch: RELEASE_3_9
Last Commit: 84cf083
Last Changed Date: 2019-05-02 11:54:14 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]NO, built version is LOWER than in internal repository!!!
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK NO, built version is LOWER than in internal repository!!!
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK NO, built version is LOWER than in internal repository!!!

Summary

Package: hypeR
Version: 1.0.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:hypeR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings hypeR_1.0.0.tar.gz
StartedAt: 2019-10-16 02:24:31 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:26:16 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 104.5 seconds
RetCode: 0
Status:  OK 
CheckDir: hypeR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:hypeR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings hypeR_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/hypeR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hypeR/DESCRIPTION’ ... OK
* this is package ‘hypeR’ version ‘1.0.0’
* 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
.hyper_enrichment: no visible global function definition for ‘is’
.hyper_enrichment: no visible global function definition for ‘p.adjust’
.hyper_enrichment: no visible global function definition for ‘rjust’
.hyper_enrichment: no visible global function definition for ‘quantile’
.hyper_enrichment: no visible global function definition for ‘phyper’
download_gsets: no visible binding for global variable ‘gs_name’
download_gsets: no visible binding for global variable ‘gene_symbol’
download_gsets: no visible binding for global variable ‘.’
download_msigdb: no visible binding for global variable ‘gs_cat’
download_msigdb: no visible binding for global variable ‘gs_subcat’
download_msigdb: no visible global function definition for
  ‘packageVersion’
hyp_plot: no visible global function definition for ‘head’
hyp_show : : no visible binding for global variable
  ‘symbols’
hyp_to_table: no visible global function definition for ‘write.table’
hypeR: no visible global function definition for ‘is’
hypeR: no visible global function definition for ‘complete.cases’
Undefined global functions or variables:
  . complete.cases gene_symbol gs_cat gs_name gs_subcat head is
  p.adjust packageVersion phyper quantile rjust symbols write.table
Consider adding
  importFrom("graphics", "symbols")
  importFrom("methods", "is")
  importFrom("stats", "complete.cases", "p.adjust", "phyper", "quantile")
  importFrom("utils", "head", "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 ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
db_get          25.630  0.870  26.696
download_msigdb 21.706  0.063  21.997
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/hypeR.Rcheck/00check.log’
for details.



Installation output

hypeR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL hypeR
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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)

Tests output

hypeR.Rcheck/tests/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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(hypeR)
> 
> test_check("hypeR")
Number of genes =  24 
Number of gene sets =  674 
Background population size =  2520 
P-Value cutoff =  1 
FDR cutoff =  0.05 
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 11 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  2.178   0.121   2.426 

Example timings

hypeR.Rcheck/hypeR-Ex.timings

nameusersystemelapsed
db_get25.630 0.87026.696
db_info0.0000.0000.001
download_gsets0.0730.0000.074
download_msigdb21.706 0.06321.997
ex_get0.0330.0000.075
hyp_plot0.3590.0160.867
hyp_show0.1560.0080.334
hyp_to_excel0.2050.0000.206
hyp_to_table0.1220.0030.125
hypeR0.1250.0000.125