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CHECK report for crossmeta on merida1

This page was generated on 2019-04-16 11:59:42 -0400 (Tue, 16 Apr 2019).

Package 348/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
crossmeta 1.8.0
Alex Pickering
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/crossmeta
Branch: RELEASE_3_8
Last Commit: 032522f
Last Changed Date: 2018-10-30 11:42:01 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: crossmeta
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:crossmeta.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings crossmeta_1.8.0.tar.gz
StartedAt: 2019-04-15 23:17:39 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:19:22 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 103.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: crossmeta.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:crossmeta.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings crossmeta_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/crossmeta.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘crossmeta/DESCRIPTION’ ... OK
* this is package ‘crossmeta’ version ‘1.8.0’
* 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 ‘crossmeta’ 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 ... NOTE
Missing or unexported objects:
  ‘crossmeta::gs.names’ ‘crossmeta::gslist’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
explore_paths : server: no visible binding for global variable ‘gslist’
explore_paths : server: no visible binding for global variable
  ‘gs.names’
Undefined global functions or variables:
  gs.names gslist
* 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
Data with usage in documentation object 'gs.names' but not in code:
  gs.names

Data with usage in documentation object 'gslist' but not in code:
  gslist

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
diff_path    7.583  0.215   7.884
symbol_annot 4.972  0.175   5.195
* 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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/crossmeta.Rcheck/00check.log’
for details.



Installation output

crossmeta.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL crossmeta
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘crossmeta’ ...
** R
** 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 (crossmeta)

Tests output

crossmeta.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(crossmeta)
> 
> test_check("crossmeta")
AnnotatingAnnotatingAnnotatingGSE1_FOO-VEH (# p < 0.05): 3 

GSE1_FOO-VEH (# p < 0.05): 3 

GSE1_FOO-VEH (# p < 0.05): 3 

══ testthat results  ═══════════════════════════════════════════════════════════
OK: 14 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 13.498   4.532  11.271 

Example timings

crossmeta.Rcheck/crossmeta-Ex.timings

nameusersystemelapsed
add_sources0.2350.0080.247
contribute0.7500.0250.783
diff_expr0.5230.0250.553
diff_path7.5830.2157.884
es_meta4.2670.3314.649
explore_paths3.1120.2313.374
get_raw0.2480.0350.902
load_diff0.2580.0040.265
load_path0.0080.0010.008
load_raw0.3070.0090.318
open_raw_illum0.0070.0000.007
path_meta0.0090.0010.010
setup_prev1.2960.0291.336
symbol_annot4.9720.1755.195