BioC 3.2: CHECK report for BaseSpaceR on oaxaca

Package: BaseSpaceR

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BaseSpaceR_1.14.0.tar.gz

StartedAt: 2016-04-22 21:58:44 -0700 (Fri, 22 Apr 2016)

EndedAt: 2016-04-22 21:59:24 -0700 (Fri, 22 Apr 2016)

EllapsedTime: 40.1 seconds

RetCode: 0

Status:  OK

CheckDir: BaseSpaceR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BaseSpaceR_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/BaseSpaceR.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BaseSpaceR/DESCRIPTION’ ... OK
* this is package ‘BaseSpaceR’ version ‘1.14.0’
* 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 ‘BaseSpaceR’ can be installed ... [3s/3s] 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 ... NOTE
'library' or 'require' call to ‘Rsamtools’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
asBamFile: no visible global function definition for ‘BamFile’
GET,ServiceURI : .local: no visible global function definition for
  ‘basicHeaderGatherer’
GET,ServiceURI : .local: no visible global function definition for
  ‘basicTextGatherer’
GET,ServiceURI : .local: no visible global function definition for
  ‘getForm’
GET,ServiceURI : .local: no visible global function definition for
  ‘curlOptions’
POST,ServiceURI : .local: no visible global function definition for
  ‘basicHeaderGatherer’
POST,ServiceURI : .local: no visible global function definition for
  ‘basicTextGatherer’
POST,ServiceURI : .local: no visible global function definition for
  ‘curlPerform’
POSTForm,ServiceURI : .local: no visible global function definition for
  ‘basicHeaderGatherer’
POSTForm,ServiceURI : .local: no visible global function definition for
  ‘basicTextGatherer’
POSTForm,ServiceURI : .local: no visible global function definition for
  ‘postForm’
POSTForm,ServiceURI : .local: no visible global function definition for
  ‘curlOptions’
getBAMs,AppResults : .local: no visible binding for global variable
  ‘BamFileList’
getFiles,AppAuth : .local : .toDisk: no visible global function
  definition for ‘CFILE’
getFiles,AppAuth : .local : .toDisk: no visible global function
  definition for ‘curlPerform’
getFiles,AppAuth : .local : .toMem: no visible global function
  definition for ‘getURLContent’
getFiles,AppAuth : .local : .toMem: no visible binding for global
  variable ‘dsize’
* 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [2s/13s] 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/BaseSpaceR.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
AppAuth-class	0.415	0.014	1.823
AppResults-class	0.002	0.000	0.002
AppSessionAuth	0.002	0.001	0.003
AppSessions-class	0.001	0.000	0.001
Coverage	0.012	0.001	0.013
Error	0.001	0.000	0.001
Files-class	0.075	0.003	0.943
FilesExtra	0.062	0.002	0.815
Genomes-class	0.111	0.004	1.235
Projects-class	0.118	0.005	1.510
Response-class	0.004	0.001	0.005
Runs-class	0.180	0.007	2.028
Samples-class	0.105	0.005	1.351
ServiceURI-class	0.000	0.000	0.001
Users-class	0.066	0.003	0.790
Variants	0.057	0.003	0.838
data-aAuth	0.030	0.002	0.412