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BioC 3.5: CHECK report for crossmeta on malbec2

This page was generated on 2017-08-16 13:17:41 -0400 (Wed, 16 Aug 2017).

Package 298/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
crossmeta 1.2.0
Alex Pickering
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/crossmeta
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: crossmeta
Version: 1.2.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings crossmeta_1.2.0.tar.gz
StartedAt: 2017-08-15 22:17:30 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:18:56 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 86.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: crossmeta.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings crossmeta_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/crossmeta.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.2.0’
* 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 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 6.62  0.108    7.29
* 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-3.5-bioc/meat/crossmeta.Rcheck/00check.log’
for details.


crossmeta.Rcheck/00install.out:

* 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)

crossmeta.Rcheck/crossmeta-Ex.timings:

nameusersystemelapsed
add_sources0.3120.0000.374
contribute0.8520.0120.890
diff_expr0.5120.0120.541
diff_path6.6200.1087.290
es_meta3.1440.0083.174
explore_paths1.7880.0161.805
get_raw0.6720.0802.269
load_diff0.2440.0000.244
load_path0.0120.0000.013
load_raw0.2400.0080.248
open_raw_illum0.0040.0040.007
path_meta0.0080.0000.007
setup_prev1.3000.0561.355
symbol_annot4.3720.0564.870