BioC 3.5: CHECK report for crossmeta on toluca2

Package: crossmeta

Version: 1.1.10

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings crossmeta_1.1.10.tar.gz

StartedAt: 2017-04-23 02:28:38 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 02:30:27 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 108.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: crossmeta.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings crossmeta_1.1.10.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/crossmeta.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘crossmeta/DESCRIPTION’ ... OK
* this is package ‘crossmeta’ version ‘1.1.10’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
diff_path    7.363  0.211   8.796
symbol_annot 5.200  0.111   6.665
* 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-3.5-bioc/meat/crossmeta.Rcheck/00check.log’
for details.

* installing *source* package ‘crossmeta’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (crossmeta)

name	user	system	elapsed
add_sources	0.285	0.008	0.300
contribute	0.901	0.020	0.935
diff_expr	0.519	0.019	0.763
diff_path	7.363	0.211	8.796
es_meta	4.232	0.275	4.564
explore_paths	2.757	0.240	3.016
get_raw	0.532	0.033	1.418
load_diff	0.192	0.004	0.196
load_path	0.008	0.000	0.008
load_raw	0.268	0.007	0.275
open_raw_illum	0.008	0.001	0.009
path_meta	0.009	0.000	0.010
setup_prev	1.049	0.026	1.081
symbol_annot	5.200	0.111	6.665