BioC 3.3: CHECK report for sbgr on zin2

Package: sbgr

Version: 1.1.1

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings sbgr_1.1.1.tar.gz

StartedAt: 2016-01-07 05:49:50 -0800 (Thu, 07 Jan 2016)

EndedAt: 2016-01-07 05:50:21 -0800 (Thu, 07 Jan 2016)

EllapsedTime: 31.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: sbgr.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings sbgr_1.1.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/sbgr.Rcheck’
* using R Under development (unstable) (2015-12-14 r69775)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sbgr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sbgr’ version ‘1.1.1’
* 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 ‘sbgr’ can be installed ... [4s/4s] 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 loading without being on the library search path ... 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 ... OK
* 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 ... WARNING
Undocumented arguments in documentation object 'billing_groups'
  ‘...’

Undocumented arguments in documentation object 'billing_invoices'
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [1s/1s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [1s/1s]
 [1s/1s] 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
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/sbgr.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
Auth-class	0.007	0.000	0.008
Metadata	0.046	0.000	0.046
Task-class	0.050	0.003	0.054
billing	0.001	0.000	0.001
billing_groups	0	0	0
billing_invoices	0	0	0
file_copy	0.001	0.000	0.001
file_delete	0.001	0.000	0.000
file_details	0.000	0.000	0.001
file_download_url	0.001	0.000	0.001
file_list	0.001	0.000	0.000
file_meta_update	0.000	0.000	0.001
misc_get_auth_token	0.001	0.000	0.001
misc_get_uploader	0	0	0
misc_make_metadata	0.000	0.000	0.001
misc_upload_cli	0.001	0.000	0.000
pipeline_add	0	0	0
pipeline_details	0.001	0.000	0.001
pipeline_list_my	0.001	0.000	0.000
pipeline_list_project	0	0	0
pipeline_list_pub	0.001	0.000	0.001
project_delete	0	0	0
project_details	0.000	0.000	0.001
project_list	0.001	0.000	0.001
project_member_add	0	0	0
project_member_delete	0.000	0.000	0.001
project_member_update	0.001	0.000	0.000
project_members	0	0	0
project_new	0.001	0.000	0.001
rate_limit	0.001	0.000	0.000
sbgapi	0	0	0
task_action	0.001	0.000	0.001
task_details	0.001	0.000	0.000
task_list	0	0	0
task_run	0.000	0.003	0.001
upload_complete_all	0.000	0.000	0.001
upload_complete_part	0	0	0
upload_delete	0	0	0
upload_info	0.001	0.000	0.001
upload_info_part	0.001	0.000	0.000
upload_init	0.000	0.000	0.001
user_list	0.001	0.000	0.001