Package: crossmeta

Version: 1.6.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:crossmeta.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings crossmeta_1.6.0.tar.gz

StartedAt: 2018-10-15 23:33:53 -0400 (Mon, 15 Oct 2018)

EndedAt: 2018-10-15 23:35:10 -0400 (Mon, 15 Oct 2018)

EllapsedTime: 77.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: crossmeta.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:crossmeta.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings crossmeta_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/crossmeta.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 ‘crossmeta/DESCRIPTION’ ... OK
* this is package ‘crossmeta’ version ‘1.6.0’
* 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 5.496  0.124   5.725
* 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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/crossmeta.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL crossmeta
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/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)

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(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 
  7.052   0.164   7.204 

name	user	system	elapsed
add_sources	0.148	0.012	0.159
contribute	0.532	0.012	0.544
diff_expr	0.444	0.004	0.515
diff_path	5.496	0.124	5.725
es_meta	2.604	0.012	2.619
explore_paths	1.744	0.012	1.758
get_raw	0.316	0.068	1.283
load_diff	0.184	0.000	0.188
load_path	0.000	0.004	0.007
load_raw	0.332	0.008	0.341
open_raw_illum	0.008	0.000	0.007
path_meta	0.008	0.000	0.006
setup_prev	1.168	0.040	1.207
symbol_annot	3.264	0.024	3.287