BioC 3.4: CHECK report for BaseSpaceR on malbec1

Package: BaseSpaceR

Version: 1.18.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings BaseSpaceR_1.18.0.tar.gz

StartedAt: 2017-04-14 21:05:47 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 21:06:20 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 32.4 seconds

RetCode: 0

Status:  OK

CheckDir: BaseSpaceR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings BaseSpaceR_1.18.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/BaseSpaceR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BaseSpaceR/DESCRIPTION’ ... OK
* this is package ‘BaseSpaceR’ version ‘1.18.0’
* 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 ... 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: no visible global function definition for
  ‘basicHeaderGatherer’
GET,ServiceURI: no visible global function definition for
  ‘basicTextGatherer’
GET,ServiceURI: no visible global function definition for ‘getForm’
GET,ServiceURI: no visible global function definition for ‘curlOptions’
POST,ServiceURI: no visible global function definition for
  ‘basicHeaderGatherer’
POST,ServiceURI: no visible global function definition for
  ‘basicTextGatherer’
POST,ServiceURI: no visible global function definition for
  ‘curlPerform’
POSTForm,ServiceURI: no visible global function definition for
  ‘basicHeaderGatherer’
POSTForm,ServiceURI: no visible global function definition for
  ‘basicTextGatherer’
POSTForm,ServiceURI: no visible global function definition for
  ‘postForm’
POSTForm,ServiceURI: no visible global function definition for
  ‘curlOptions’
getBAMs,AppResults: no visible binding for global variable
  ‘BamFileList’
getFiles,AppAuth : .toDisk: no visible global function definition for
  ‘CFILE’
getFiles,AppAuth : .toDisk: no visible global function definition for
  ‘curlPerform’
getFiles,AppAuth : .toMem: no visible global function definition for
  ‘getURLContent’
getFiles,AppAuth : .toMem: no visible binding for global variable
  ‘dsize’
Undefined global functions or variables:
  BamFile BamFileList CFILE basicHeaderGatherer basicTextGatherer
  curlOptions curlPerform dsize getForm getURLContent postForm
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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
  ‘/home/biocbuild/bbs-3.4-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	0.304	0.044	0.871
AppResults-class	0.004	0.000	0.001
AppSessionAuth	0.004	0.000	0.002
AppSessions-class	0.000	0.000	0.002
Coverage	0.016	0.000	0.015
Error	0.000	0.000	0.001
Files-class	0.168	0.016	0.683
FilesExtra	0.132	0.028	0.583
Genomes-class	0.196	0.020	0.947
Projects-class	0.200	0.012	0.848
Response-class	0.004	0.000	0.004
Runs-class	0.236	0.036	1.291
Samples-class	0.256	0.008	1.016
ServiceURI-class	0.000	0.000	0.001
Users-class	0.112	0.004	0.495
Variants	0.132	0.000	0.560
data-aAuth	0.084	0.008	1.768